Haplogroup E-M96

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Haplogroup E
Possible time of origin65,200 years BP,[1] 69,000 years BP,[2] or 73,000 years BP[3]
Coalescence age52,300 years BP[1]
Possible place of originEast Africa,[4][5][6][3] West Africa,[7] or Eurasia[8][9]
DescendantsE-P147, E-M75
Defining mutationsL339, L614, M40/SRY4064/SRY8299, M96, P29, P150, P152, P154, P155, P156, P162, P168, P169, P170, P171, P172, P173, P174, P175, P176

Haplogroup E-M96 is a human Y-chromosome DNA haplogroup. It is one of the two main branches of the older and ancestral haplogroup DE, the other main branch being haplogroup D. The E-M96 clade is divided into two main subclades: the more common E-P147, and the less common E-M75.


Underhill (2001) proposed that haplogroup E may have arisen in East Africa.[10] Some authors as Chandrasekar (2007), accept the earlier position of Hammer (1997) that Haplogroup E may have originated in West Asia,[11] given that:

  • E is a clade of Haplogroup DE, with the other major clade, haplogroup D, being exclusively distributed in Asia.
  • DE is a clade within M168 with the other two major clades, C and F, considered to have already a Eurasian origin.

However, several discoveries made since the Hammer articles are thought to make an Asian origin less likely:

  1. Underhill and Kivisild (2007) demonstrated that C and F have a common ancestor meaning that DE has only one sibling which is non-African.[12]
  2. DE* is found in both Asia and Africa, meaning that not only one, but several siblings of D are found in Asia and Africa.
  3. Karafet (2008), in which Hammer is a co-author, significantly rearranged time estimates leading to "new interpretations on the geographical origin of ancient sub-clades".[13] Amongst other things this article proposed a much older age for haplogroup E-M96 than had been considered previously, giving it a similar age to Haplogroup D, and DE itself, meaning that there is no longer any strong reason to see it as an offshoot of DE which must have happened long after DE came into existence and had entered Asia.[13]

Kohl et al. (2009) suggested a West African origin for haplogroup E, stating: "From the 20 main haplogroups in the Y-chromosomal haplogroup tree, only 5 were detected in the analysed Amharic population in Ethiopia. Haplogroup A is near the roots of the tree and is only found among males on the African continent. The major haplogroup detected was E. Haplogroup E has its origin in West Africa. Due to immigration haplogroup A, which originally dominated in Ethiopia, has been partly replaced."[7]

In 2015 Poznik and Underhill have claimed haplogroup E, arose outside Africa, arguing that, "This model of geographical segregation within the CT clade requires just one continental haplogroup exchange (E to Africa), rather than three (D, C, and F out of Africa). The timing of this putative return to Africa, between the emergence of haplogroup E and its differentiation within Africa by 58 kya, is consistent with proposals, based on non–Y chromosome data, of abundant gene flow between Africa and Arabia 50–80 kya."[8]

In 2015 Trobetta et al. suggested an East African origin for haplogroup E, stating: "our phylogeographic analysis, based on thousands of samples worldwide, suggests that the radiation of haplogroup E started about 58 ka, somewhere in sub-Saharan Africa, with a higher posterior probability (0.73) for an eastern African origin."[6]

A Eurasian center of origin and dispersal for haplogroup E has also been hypothesized by Cabrera et al. (2018) based on the similar age of the clade's parent haplogroup DE and the mtDNA haplogroup L3. According to this hypothesis, after an initial Out-of-Africa migration of early anatomically modern humans around 125 kya, E-carrying males are thus proposed to have back-migrated from the paternal haplogroup's place of origin in Eurasia around 70 kya along with females bearing the maternal haplogroup L3, which the study also hypothesizes to have originated in Eurasia. These new Eurasian lineages were then suggested to have largely replaced the old autochthonous male and female African lineages.[9]

A 2019 study by Haber et al. supports an African origin for haplogroup E (based on an analysis of the Y-chromosomal phylogenetic structure, haplogroup divergence times, and the recently discovered haplogroup D0 found in three Nigerians, an additional branch of the DE lineage diverging early from the D branch). The authors support an African origin for DE (parent haplogroup of E) with E and D0 also originating in Africa, along with the migration out of Africa of the three lineages (C, D and FT) that now form the vast majority of non-African Y chromosomes. The early divergence dates found in the study for DE, E, and D0 (all dated from about 71-76 kya), which are determined to predate the migration out-of-Africa of the ancestors of Eurasians (dated to ca. 50-60 kya), are also considered by the authors to support an African origin for those haplogroups.[3]

Ancient DNA[edit]

Pre-Pottery Neolithic B remains were found to have carried haplogroup E (1/7; ~14%).[14]

At Nyarindi Rockshelter, in Kenya, there were two individuals, dated to the Later Stone Age (3500 BP); one carried haplogroup L4b2a and another carried haplogroup E (E-M96, E-P162).[15][16]

At Kindoki, in the Democratic Republic of Congo, there were three individuals, dated to the protohistoric period (230 BP, 150 BP, 230 BP); one carried haplogroups E1b1a1a1d1a2 (E-CTS99, E-CTS99) and L1c3a1b, another carried haplogroup E (E-M96, E-PF1620), and the last carried haplogroups R1b1 (R-P25 1, R-M415) and L0a1b1a1.[15][16]


Most members of haplogroup E-M96 belong to one of its identified subclades, and the E-M96(xE-P147, E-M75) is rare. E1a and E-M75 are found almost exclusively in Africa. By looking at the major subclade frequencies, five broad regions of Africa can be defined: East, Central, North, Southern and West. The division can be distinguished by the prevalence of E-M2 in East, Central, Southern and West Africa, E-M78 in East Africa and E-M81 in North Africa. E-M2 is the most prevalent subclade of E in Africa. It is observed at high frequencies in all African regions from moderate to high. E-M215 (especially its subclades M78 and M81) is found at high frequencies in North East Africa and North Africa and is the only subclade that is found in Europe and Asia at significant frequencies. E-M215 is common among Afro-Asiatic speakers in the Near East and North Africa as well as among some Nilo-Saharan and Niger–Congo speakers in North East Africa and Sudan. E-M215 is far less common in West, Central, and Southern Africa, though it has been observed among some Khoisan speakers[17] and among Niger–Congo speakers in Senegambia,[18] Guinea-Bissau,[19] Burkina Faso,[20] Ghana, Gabon,[21] the Democratic Republic of the Congo, Rwanda,[22] Namibia, and South Africa.

Haplogroup E and its major subclades.



Paragroup E-M96* refers to lineages belonging to the E clade but which cannot be classified into any known branch. E(xE1-P147, E2-M75) - that is, E which has tested negative for both P147 and M75 - has been reported in 2 Amharas from Ethiopia,[23] in 2 men from Saudi Arabia,[24] and in a single Bantu-speaking male from South Africa.[13] E(xE1a-M33, E1b1-P2, E2-M75) was reported among several Southern African populations and in an Egyptian man;[25] E(xE1a-M33, E1b1a1-M2, E1b1b-M215, E2-M75) has been observed amongst pygmies and Bantu from Cameroon and Gabon;[21] and E(xE1a-M33, E1b1a1-M2, E1b1b1-M35, E2-M75) has been found in several Lebanese,[26] in Burkina Faso,[27] and a Fulbe man from Niger.[28]

Recently it was discovered that 3 East African men previously classified only as E*-M96 could be assigned to a new branch, E-V44, which is a sister branch to E1-P147; E-P147 and E-V44 share the V3725 mutation, making E2-M75 and E-V3725 the two known primary branches of E.[29] It is not known whether or not some (or all) other E*(xE1, E2) would fall into V44 as well.


E-P147 (also known as E1) is by far the most numerous and widely distributed branch of E-M96. It has two primary branches: E-M132 (E1a) and E-P177 (E1b).

Within Haplogroup E-P177, Haplogroup E-P2 (E1b1) – a subclade of E-P177 – is not only the most frequent variant of E-M96, but is also the most common Y-DNA lineage in Africa. It is also the only subclade of E-M96 found in significant numbers in West Asia and Europe.

A prolific primary branch of E-P2, Haplogroup E-M215 (E1b1b) is distributed in high frequencies from East Africa, through North Africa into Western Asia and Southern Europe. It is also found at significant levels among populations native to Southern Africa and throughout Western Europe.


E-M75 is present throughout Subequatorial Africa, particularly in the African Great Lakes and Central Africa. The highest concentration of the haplogroup has been found among the Alur (66.67%),[25] Hema (38.89%),[25] Rimaibe (27.03%),[20] Mbuti (25.00%),[20] Daba (22.22%),[20] Eviya (20.83%),[21] Zulu (20.69%),[25] and Kenyan Bantus (17.24%).[22]

Haplogroup E-M75(xM41,M54) has been found in 6% (1/18) of Dama from Namibia,[25] 4% (1/26) of Ganda from Uganda,[25] 3% (1/39) of Mandinka from Gambia/Senegal,[25] and 2% (1/49) of Shona from Zimbabwe.[25]

Family Tree DNA shows numerous persons of Haplogroup E-M75 claiming origins from the Arabian Peninsula (most from Saudi Arabia, but also from Bahrain, Kuwait, Yemen, and United Arab Emirates).[30] Sampling bias does not allow for meaningful percentages, but the presences of the haplogroup is solidly attested.


Phylogenetic history[edit]

Prior to 2002, there were in academic literature at least seven naming systems for the Y-Chromosome Phylogenetic tree. This led to considerable confusion. In 2002, the major research groups came together and formed the Y-Chromosome Consortium (YCC). They published a joint paper that created a single new tree that all agreed to use. Later, a group of citizen scientists with an interest in population genetics and genetic genealogy formed a working group to create an amateur tree aiming at being above all timely. The table below brings together all of these works at the point of the landmark 2002 YCC Tree. This allows a researcher reviewing older published literature to quickly move between nomenclatures.

YCC 2002/2008 (Shorthand) (α) (β) (γ) (δ) (ε) (ζ) (η) YCC 2002 (Longhand) YCC 2005 (Longhand) YCC 2008 (Longhand) YCC 2010r (Longhand) ISOGG 2006 ISOGG 2007 ISOGG 2008 ISOGG 2009 ISOGG 2010 ISOGG 2011 ISOGG 2012
E-P29 21 III 3A 13 Eu3 H2 B E* E E E E E E E E E E
E-M33 21 III 3A 13 Eu3 H2 B E1* E1 E1a E1a E1 E1 E1a E1a E1a E1a E1a
E-M44 21 III 3A 13 Eu3 H2 B E1a E1a E1a1 E1a1 E1a E1a E1a1 E1a1 E1a1 E1a1 E1a1
E-M75 21 III 3A 13 Eu3 H2 B E2a E2 E2 E2 E2 E2 E2 E2 E2 E2 E2
E-M54 21 III 3A 13 Eu3 H2 B E2b E2b E2b E2b1 - - - - - - -
E-P2 25 III 4 14 Eu3 H2 B E3* E3 E1b E1b1 E3 E3 E1b1 E1b1 E1b1 E1b1 E1b1
E-M2 8 III 5 15 Eu2 H2 B E3a* E3a E1b1 E1b1a E3a E3a E1b1a E1b1a E1b1a E1b1a1 E1b1a1
E-M58 8 III 5 15 Eu2 H2 B E3a1 E3a1 E1b1a1 E1b1a1 E3a1 E3a1 E1b1a1 E1b1a1 E1b1a1 E1b1a1a1a E1b1a1a1a
E-M116.2 8 III 5 15 Eu2 H2 B E3a2 E3a2 E1b1a2 E1b1a2 E3a2 E3a2 E1b1a2 E1b1a2 E1ba12 removed removed
E-M149 8 III 5 15 Eu2 H2 B E3a3 E3a3 E1b1a3 E1b1a3 E3a3 E3a3 E1b1a3 E1b1a3 E1b1a3 E1b1a1a1c E1b1a1a1c
E-M154 8 III 5 15 Eu2 H2 B E3a4 E3a4 E1b1a4 E1b1a4 E3a4 E3a4 E1b1a4 E1b1a4 E1b1a4 E1b1a1a1g1c E1b1a1a1g1c
E-M155 8 III 5 15 Eu2 H2 B E3a5 E3a5 E1b1a5 E1b1a5 E3a5 E3a5 E1b1a5 E1b1a5 E1b1a5 E1b1a1a1d E1b1a1a1d
E-M10 8 III 5 15 Eu2 H2 B E3a6 E3a6 E1b1a6 E1b1a6 E3a6 E3a6 E1b1a6 E1b1a6 E1b1a6 E1b1a1a1e E1b1a1a1e
E-M35 25 III 4 14 Eu4 H2 B E3b* E3b E1b1b1 E1b1b1 E3b1 E3b1 E1b1b1 E1b1b1 E1b1b1 removed removed
E-M78 25 III 4 14 Eu4 H2 B E3b1* E3b1 E1b1b1a E1b1b1a1 E3b1a E3b1a E1b1b1a E1b1b1a E1b1b1a E1b1b1a1 E1b1b1a1
E-M148 25 III 4 14 Eu4 H2 B E3b1a E3b1a E1b1b1a3a E1b1b1a1c1 E3b1a3a E3b1a3a E1b1b1a3a E1b1b1a3a E1b1b1a3a E1b1b1a1c1 E1b1b1a1c1
E-M81 25 III 4 14 Eu4 H2 B E3b2* E3b2 E1b1b1b E1b1b1b1 E3b1b E3b1b E1b1b1b E1b1b1b E1b1b1b E1b1b1b1 E1b1b1b1a
E-M107 25 III 4 14 Eu4 H2 B E3b2a E3b2a E1b1b1b1 E1b1b1b1a E3b1b1 E3b1b1 E1b1b1b1 E1b1b1b1 E1b1b1b1 E1b1b1b1a E1b1b1b1a1
E-M165 25 III 4 14 Eu4 H2 B E3b2b E3b2b E1b1b1b2 E1b1b1b1b1 E3b1b2 E3b1b2 E1b1b1b2a E1b1b1b2a E1b1b1b2a E1b1b1b2a E1b1b1b1a2a
E-M123 25 III 4 14 Eu4 H2 B E3b3* E3b3 E1b1b1c E1b1b1c E3b1c E3b1c E1b1b1c E1b1b1c E1b1b1c E1b1b1c E1b1b1b2a
E-M34 25 III 4 14 Eu4 H2 B E3b3a* E3b3a E1b1b1c1 E1b1b1c1 E3b1c1 E3b1c1 E1b1b1c1 E1b1b1c1 E1b1b1c1 E1b1b1c1 E1b1b1b2a1
E-M136 25 III 4 14 Eu4 H2 B E3b3a1 E3b3a1 E1b1b1c1a E1b1b1c1a1 E3b1c1a E3b1c1a E1b1b1c1a1 E1b1b1c1a1 E1b1b1c1a1 E1b1b1c1a1 E1b1b1b2a1a1

Research publications[edit]

The following research teams per their publications were represented in the creation of the YCC tree.

Phylogenetic trees[edit]

This phylogenetic tree of haplogroup subclades is based on the Y-Chromosome Consortium (YCC) Tree,[31] the ISOGG Y-DNA Haplogroup Tree,[32] and subsequent published research.

E (M96
E1 (P147)

E1a (M132)

E1b1 (P2)
E1b1a (V38)

E1b1a1 (M2)

E1b1a2 (M329)

E1b1b (M215)

E1b1b1a (V68)

E1b1b1b (Z827)

E2 (M75)

See also[edit]


Y-DNA E subclades[edit]

Y-DNA backbone tree[edit]


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  30. ^ Family Tree DNA public haplotree, Haplogroup E-M75
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  32. ^ International Society of Genetic Genealogy. "Y-DNA Haplogroup Tree". Retrieved 20 December 2012.

Sources for conversion tables[edit]

Further reading[edit]

External links[edit]

Phylogenetic tree and distribution maps of Y-DNA haplogroup E[edit]